Congenital Malformations of the Digestive Tract

Occasionally, babies can be born with defects along their digestive tract. Most commonly, these defects are undeveloped or incorrectly positioned organs that prevent the digestive system from functioning. While these conditions are rare, they’re also serious and usually require surgery.

Key Facts

  • Digestive malformations can occur anywhere from the esophagus to the anus. There are many different types, but they most frequently cause blockages of the digestive tract.
  • Specific malformations include undeveloped organs (atresia), misaligned and/or twisted organs (malrotation and volvulus), and undeveloped nerves (Hirschsprung’s disease).
  • Symptoms will depend on the specific malformation and its location. Most malformations can be surgically treated and have good long-term outcomes.


Congenital digestive malformations occur when organs do not develop properly while a fetus is still in the womb. The underlying cause of these malformations is still unknown, although some experts believe there may be a genetic link.

The following are some of the most common malformations and how they form:

Atresia and Stenosis

These cause complete blockage (atresia) and partial blockage (stenosis) of the digestive tract. There are several different types:

  • Anorectal: An anal opening that’s narrow or enclosed by a layer of tissue or skin.
  • Biliary: Bile ducts that become progressively narrow and/or blocked.
  • Esophageal: An esophagus that narrows and/or ends before reaching the stomach.
  • Gastric: The opening between the stomach and small intestine is blocked by a layer of tissue or is separated completely.
  • Intestinal: A segment of the small or large intestine is narrow or completely separate from the rest of the digestive tract.

Malrotation and Volvulus

As a fetus develops, the organs that make up its digestive tract gradually rotate to their final position. A malrotation refers to when this rotation does not happen correctly. Most often, this occurs in the small intestine. Malrotations may or may not cause symptoms.

Volvulus is a severe complication that can result from a malrotation. It refers to when organs become twisted in such a way that blood flow is blocked or the digestive tract is obstructed.

Hirschsprung’s Disease

The large intestine relies on nerves within its walls (called ganglia nerves) to contract and push food toward the anus. In Hirschsprung’s disease, these nerves have not formed in a section of the large intestine. This prevents the intestine from contracting normally, causing food to build up and blockages to form.

Other Malformations

Other congenital malformations of the digestive tract include the following:

  • Abdominal Wall Defects: When a section of the digestive tract forms outside of the baby’s body due to an abnormality in the abdominal wall.
  • Duplication Cysts: When an abnormal “extra” portion of the intestines form and attach somewhere along the digestive tract.
  • Tracheoesophageal Fistula: When a portion of the esophagus connects to the trachea (windpipe).


Symptoms will depend on the specific malformation, where it is located, and its severity. Every child will present symptoms differently.

Atresia and Stenosis

The following are some general symptoms of atresia and stenosis:

  • Constipation
  • Coughing
  • Difficulty eating
  • Jaundice (yellowing of eyes and skin)
  • Swollen abdomen
  • Vomiting

Malrotation and Volvulus

Malrotation by itself may not cause any symptoms. However, malrotation with volvulus can be a life-threatening condition. It may include the following symptoms:

  • Abdominal pain
  • Bloody stools
  • Constipation
  • Diarrhea
  • Drawing up of legs
  • Failure to thrive
  • Rapid breathing
  • Rapid heart rate
  • Rectal bleeding
  • Swollen abdomen
  • Vomiting bile 

Hirschsprung’s Disease

In severe cases of Hirschsprung’s disease, the most obvious symptom will be a failure to have a bowel movement in the first 48 hours of life. Other symptoms may include the following:

  • Constipation
  • Diarrhea
  • Fatigue
  • Swollen abdomen
  • Vomiting


Most congenital digestive tract malformations can be diagnosed before birth using a prenatal ultrasound. This test uses soundwaves to give doctors a detailed image of the fetus and any possible malformations. 

The following are some ways to diagnose digestive malformations after birth:

  • Biopsy: Often used to diagnose Hirschsprung’s disease, this removes a sample of cells from the digestive tract to test for any abnormalities.
  • Blood Tests: This measures electrolyte levels. An abnormal level may indicate digestive tract issues.
  • Imaging Tests: These create a detailed image of the digestive tract and/or abdomen so that doctors can detect any malformations. They may include a computed tomography (CT) scan, a magnetic resonance imaging (MRI) test, and an x-ray using barium, a dye that helps illuminate the digestive tract.
  • Sigmoidoscopy: This inserts a flexible, lighted tube into the large intestine through the rectum so that doctors can detect any abnormalities.
  • Stool Samples: These are used to look for blood in the stools.


The majority of digestive tract malformations require surgery. This involves accessing the defect, repairing the obstruction or aligning the organs, then closing the incision. There are two general types of surgery:

  • Laparoscopic: This is a minimally invasive type of surgery that uses existing openings, such as the anus, or very small incisions to access the digestive organs. It’s usually used for more minor defects.
  • Open: This is a more invasive surgery in which a larger incision is made in the abdomen or elsewhere in order to access the digestive organs. It’s usually used when repairing more severe defects.


With proper treatment, the outlook for children born with digestive malformations is usually very good. Blockages and/or incorrectly placed organs can be surgically repaired, allowing the child to grow and develop normally.

In some cases, such as when a damaged portion of an organ must be removed, there may be long-term problems. These can include minor issues such as constipation to more severe problems such as a difficulty absorbing nutrients. Because of this, it may be necessary to meet regularly with the following specialists to ensure everything is functioning normally:

  • Gastroenterologist: This is a doctor that specializes in digestive tract issues. They can help diagnose additional problems and come up with treatment plans.
  • Nutritionist: This is a specialist that can help develop proper diets following surgery for a digestive tract malformation. This can help avoid potential issues such as constipation and enterocolitis (infection and inflammation of the intestine).

Next Steps

Columbia’s Pediatric Surgery program can help diagnose most congenital digestive tract issues before birth. We will then create a treatment plan to repair the issue as soon as possible so that your child can continue to grow and develop normally.

Call us at (212) 342-8585 or use our online form to schedule an appointment.

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